Generally, follow the installation guide for your cooler. Some have specific features that can only be accessed through whatever system they provide. EG, corsair use corsair link.

The PUMP AIO header has a higher output (think this is 2amps on the X370 Prime) where as the CPU fan header has a standard 1a output. they still behave as normal fan headers.

I assume the included hub is plugged directly into a power source? (molex/sata?)

For sake of warranty purposes, I would suggest running with recommended installation, but if you wanted to risk it, use the fans with the cpu/cpu opt, and the pump with the AIO header, but again, its at your own risk.